Burble Hekelot - Another former member of Phantom's Zan'ei Army. Burble is a frog-like boss who attacks (sometimes while hanging from the ceiling) with his tongue, launches missiles from his back, spits bubbles, and turns into a big ball to smash Zero.

Kuwagust Anchus - A member of Harpuia's Rekku Army. As he was built with the same technology of Herculious Anchortus, they are known as brother Reploids. When the player faces him again in the final stage, Zero fights both him and Herculious together.

Elpizo - Leader of the Resistance and the final boss of the game. He absorbs the Dark Elf and transforms into a terrifying menace.

One year has passed since Zero defeated Copy X. He has since spent his time wandering the desert defeating wave after wave of Pantheons. As the game opens, Zero wearily makes his way through a sand-storm wrapped in a tattered cloak. As the sands die down he realizes he is once more being chased by enemies. Despite being in disrepair, with cracked armor and broken weapons (his rod and shield are useless), his cloak is thrown to the winds and his Buster Shot is drawn in defense.

"This isn't fun anymore," he says, after dispatching the first of an endless wave of enemies.

Elsewhere, the three surviving members of the Four Guardians (Phantom self-destructed trying to stop Zero's assault on Area X) assumed command of Neo Arcadia, with Harpuia as the leader. Copy X's death was covered up, as the humans revered him as their savior.

Some time later, a barely-functioning Zero is brought to the newly-completed Resistance Base (strangely, by Harpuia), and Zero learns that the conflict between Neo Arcadia and the Resistance has still continued during his absence. While he was gone, Ciel was working on a way to solve the energy crisis that led to all of the problems with Neo Arcadia in the first place. However, the Resistance leader, a reploid named Elpizo, believing that Ciel's search was futile, leads a failed assault on Neo Arcadia, from which he is the only survivor. Driven mad by this, he declares his desire to harness the power of the legendary Dark Elf, which had brought about the Elf Wars a century ago.

Elpizo, using the powers granted by unsealing a portion of the power of the Dark Elf, invades Neo Arcadia and single-handedly breaks into the temple where the body of the real X, revered by all in the utopia, is kept. As it turned out, X had ended the Elf Wars by sealing the Dark Elf away with his body, thus leading to his disappearance. Despite the Guardians' and Zero's resistance, Elpizo succeeds in destroying X's body, which unseals the Dark Elf, and Elpizo begins to absorb its powers.

Zero manages to stop Elpizo from unleashing the Dark Elf on the world. As Elpizo lies on the floor dying, he apologizes for everything he's done. Amazingly, the Dark Elf saves him by turning him into a cyber elf and convincing Elpizo that she is not truly evil. As the two elves depart, Mega Man X himself arrives and tells Zero about the Dark Elf. She was originally made to be a savior, but was cursed by a man named Dr. Weil, and used...

...Meanwhile, in a mysterious area, a voice calls for someone named Omega to act.

This game follows almost the exact same game-play rules as its predecessor. Once again, players take control of the Reploid known as Zero, and lead him through various levels in the battle against the forces of Neo Arcadia.

The controls are identical to that in the previous game, with players given the option to assign functions to the buttons they are most comfortable using. Once again, players are given a variety of weapons that include the Z-Saber, the Buster Shot, and the Shield Boomerang. Zero's skill levels with these weapons are minimal at first, but they will strengthen with repeated use.

The Triple Rod from the previous game, however, has been replaced with the Chain Rod. It can be used to pull enemies or objects closer, pull shields off enemies or if latched on to an immovable object, to swing over chasms.

Cyber Elves also make a reappearance and once again, they come in three types, Nurse, Animal and Hacker. Unlike the previous game, where all of the Sub-Tanks could only be obtained from using four special Nurse Cyber Elves, two Sub-Tanks are hidden in the game in two of the eight selectable stages.

Instead of selecting from a list of missions, the traditional Stage Select option found in the original Mega Man and the Mega Man X games makes a return, although the player can only select from four at a time. Unlike in the previous game, none of the stages are linked.

The second game introduces the concept of various forms, which can be earned by meeting certain criteria throughout the game, ranging from killing twenty enemies in a stage with a dashing slash technique to getting twenty-five energy capsules in one stage.

Normal Form (Red) - Zero's basic form. The player starts the game with this. It has basic stats in all areas. No glaring weaknesses or strengths. It uses the standard 3-hit Z-Saber combo of "back, forward, overhead".

Energy Form (Yellow) - This form makes energy crystals appear more often. The Buster Shot and Z-saber gets an attack boost, while sacrificing some speed. The player have to grab twenty-five energy capsules in mission to awaken this form.

X Form (Blue) - The Buster Shot gains an attack boost, and also allows a rapid fire capability. Like the Erase form, it cannot perform Z-Saber combos and instead uses only the forward slash. It is named after X because of X's fighting-style (which relied heavily on the buster) in the Mega Man X series. Zero also uses the Z-Saber the way X uses it in Mega Man X6. The player need to kill fifty enemies in mission with the Buster Shot to awaken this form.

Defense Form (Green) - Zero's defense is increased to its maximum, as well as sacrificing attack power in the process (except for the shield boomerang, which gains an attack boost). The player need to kill twenty enemies in mission with Shield Boomerang to awaken this form.

Erase Form (Pink) - The Erase Form allows the Z-Saber and Shield Boomerang to nullify enemy shots. It cannot use saber combos, instead it always uses the forward slash. The player need to ricochet thirty shots back at enemies with the Shield Boomerang in mission to awaken this form.

Active Form (Orange) - Zero's speed is increased to the maximum. The Z-Saber cannot perform combos, and will instead use only the back slash. However, this form enables Zero to perform rolling attacks with the saber while jumping or dashing. The rolling attacks, while not very powerful, can strike multiple times. The player need to kill twenty enemies in mission with the Z-Saber while dashing to awaken this form.

Power Form (Purple) - Zero's power is boosted to its limit, while sacrificing some speed in the process. This form also negates the three-hit Z Saber combo in favor of a single overhead slash. The player should pull anything thirty times in mission with the Chain Rod in order to awaken this form.

Rise Form (Grey) - More or less identical to the Normal form, but the 3rd (overhead) slash in the Z-saber combo is replaced by the rising slash, which is a little faster, and is given an attack boost. The player need to kill twenty enemies in mission with the jumping slash to awaken this form.

Proto Form (Black) - Zero gains an attack increase to all weapons, but besides the Shield Boomerang none of them can be charged, and the Z-Saber cannot perform combos. It will use only the back slash. Zero also takes twice the normal damage from enemy attacks. Unlike the other Hard modes in the Zero games, Zero 2 makes the player use only the Proto Form, limiting all weapons to their base attacks. The one thing that deviates is that the Charge Shot(s) is absent in it, as all other Hard Modes have it. Unlike the Galacta Armor from the fourth game, it doesn't deal 2x damage.

Ultimate Form (Glowing Crimson) - This form gives all of Zero's weapons an increase in power, as well as raising his speed and defense. This form also allows the player to input simplistic Street Fighter-esque commands to execute charged attacks instantly. This form also appears in the first, third and fourth game. The player need to level up and use every single cyber-elf in game and then complete the game in order to awaken this form (can be unlocked at the same time as the Proto Form).

Absent in the previous Mega Man Zero game are the EX Skills. They are abilities or techniques that can be earned from defeating a boss, which were a staple of the original Mega Man games. The only catch is that to earn the EX Skills in Mega Man Zero 2, Zero must be at A or S Rank when he defeat the boss, as that is the only time when the bosses will use their EX Skills.

As in Mega Man Zero, the rank is dependent on how well the player finish a particular stage with points being awarded for not taking damage, for defeating enemies and for being quick and for not using Cyber Elves.

Just like in the first game, a "New Game Plus" can be played by beating the game and loading the completed save file. In the new game, Zero will start with all activated Cyber Elves used from the previous game still in effect (the penalties, however, will still remain). Zero will also get to keep any EX Skills and alternate forms that he earned in the previous game as well.

Additional modes can also be unlocked under proper conditions.

Hard Mode is unlocked by beating the game once. Players need to hold L when selecting to start a New Game. In Hard Mode, Zero is in his "Proto Form", which doubles his attack strength but halves his defense. In addition, Zero's weapons cannot increase in strength and he cannot earn any EX skills or alternate forms.

Beating Hard Mode will unlock a special "Image Gallery" option. The player need to hold L and Select when selecting New Game to enter it.

Unlike the other games in the series, there is no Ultimate Mode to be unlocked. However, an "Ultimate Form" can be unlocked by leveling and using every Cyber Elf in the game. It increases all of Zero's stats and also allows him to use full-charge attacks instantly by means of simplistic button combos.